gdPlot             package:GenomeGraphs             R Documentation

_g_d_P_l_o_t _i_s _t_h_e _m_a_i_n _p_l_o_t_t_i_n_g _f_u_n_c_t_i_o_n _o_f _t_h_e _G_e_n_o_m_e_G_r_a_p_h_s _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     gdPlot is the main plotting function of the GenomeGraphs package. 
     A collection of objects are given as a list and these will then be
     plotten in the order given.

_U_s_a_g_e:

     gdPlot(gdObjects, minBase = NA, maxBase = NA, highlightRegions = NULL)

_A_r_g_u_m_e_n_t_s:

gdObjects: This is either a list of 'gdObjects' which will be plotted
          from top to bottom or a single 'gdObjects' to be plotted. 

 minBase: 'minBase' defines the minimum base that will be plotted, if
          ommitted a minimum is determined from the objects in
          'gdObjects' if possible. 

 maxBase: 'maxBase' defines the maximum base that will be plotted,if
          ommitted a minimum is determined from the objects in
          'gdObjects' if possible. 

highlightRegions: 'highlightRegions' defines a set of regions to
          overlay as rectangles on the plot. This argument is either a
          list or a single HighlightRegion object.  

_A_u_t_h_o_r(_s):

     Steffen Durinck and James Bullard

_R_e_f_e_r_e_n_c_e_s:

     http://www.stat.berkeley.edu/~steffen/

_E_x_a_m_p_l_e_s:

     data("dummyData", package="GenomeGraphs")

     minbase = min(probestart)
     maxbase = max(probestart)

     mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")

     genesplus = new("GeneRegion", start = minbase, end = maxbase, strand = "+", chromosome = "3", biomart=mart)
     genesmin = new("GeneRegion", start = minbase, end = maxbase, strand = "-", chromosome = "3", biomart=mart)

     seg <- new("Segmentation", segments = segments, 
                segmentStart = segStart, segmentEnd = segEnd, dp = DisplayPars(color = "dodgerblue2", lwd=2,lty = "dashed"))

     cop <- new("GenericArray", intensity  = cn, probeStart = probestart, 
                segmentation =  seg, dp = DisplayPars(size=3, color = "seagreen", type="dot"))

     ideog = new("Ideogram", chromosome = "3")
     expres = new("GenericArray", intensity = intensity, probeStart = exonProbePos, dp = DisplayPars(color="darkred", type="point"))
     genomeAxis = new("GenomeAxis", add53 = TRUE, add35=TRUE)
     gdPlot(list(ideog,expres,cop,genesplus,genomeAxis,genesmin), minBase = minbase, maxBase =maxbase)

